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remove hardcoded feature number - #20

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Cajac102 wants to merge 96 commits into

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flex_feature_number

Commits on Aug 28, 2024
- Initial commit
  RobbinBouwmeester
  authored
  b21bec3
- Intial commit
  RobbinBouwmeester
  committed
  f983c44
Commits on Sep 19, 2024
- Remove from main and split functions
  RobbinBouwmeester
  committed
  e19ef27
Commits on Sep 21, 2024
- Refactoring second round - split into folders+files+functions
  RobbinBouwmeester
  committed
  11dfbf7
- More general refactoring
  RobbinBouwmeester
  committed
  a6081d3
- Pickle in specific directory
  RobbinBouwmeester
  committed
  306e520
Commits on Sep 22, 2024
- Further refactoring - main function
  RobbinBouwmeester
  committed
  06e700a
Commits on Nov 3, 2024
- More refractoring, prep for stepwise opt
  RobbinBouwmeester
  committed
  b0cf793
Commits on Feb 4, 2025
- Various changes, mostly debugging
  RobbinBouwmeester
  committed
  fe3ee24
- Modified
  RobbinBouwmeester
  committed
  09e92d4
Commits on Feb 5, 2025
- Sep corr and others
  RobbinBouwmeester
  committed
  d2134b5
Commits on Feb 6, 2025
- New pickling strategy
  RobbinBouwmeester
  committed
  3d24413
- CMD parser updates
  RobbinBouwmeester
  committed
  704dcdd
Commits on Feb 13, 2025
- Changes to MS1 matching and writing temp files
  RobbinBouwmeester
  committed
  dafcb1b
Commits on Feb 14, 2025
- New correlation calculation
  RobbinBouwmeester
  committed
  fc883d2
Commits on Feb 20, 2025
- Major changes diff calc
  RobbinBouwmeester
  committed
  54270ee
Commits on Aug 3, 2025
- Major test coverage improvements and workflow enhancements
  RobbinBouwmeester
  committed
  37882bc
- Add comprehensive GitHub Actions CI/CD workflows
  RobbinBouwmeester
  committed
  48e90f4
- Fix license information: Change from MIT to Apache-2.0
  RobbinBouwmeester
  committed
  ab48940
- Fix setuptools configuration in pyproject.toml
  RobbinBouwmeester
  committed
  1e87c53
- fix testing
  RobbinBouwmeester
  committed
  6383358
- Add missing dependencies for CI tests
  RobbinBouwmeester
  committed
  17f5494
- Add missing tensorflow and workflow dependencies
  RobbinBouwmeester
  committed
  5de20fe
- workflow maker
  RobbinBouwmeester
  committed
  e36a349
Commits on Aug 4, 2025
- changes to dependencies
  RobbinBouwmeester
  committed
  2d7b192
- remove csv
  RobbinBouwmeester
  committed
  f02e516
- formatting and style changes
  RobbinBouwmeester
  committed
  592c788
- formatting
  RobbinBouwmeester
  committed
  5483508
- remove useless .md
  RobbinBouwmeester
  committed
  e3ffeee
- Update README.md
  RobbinBouwmeester
  authored
  b015b4e
Commits on Aug 5, 2025
- runnable for me
  rodvrees
  committed
  1697d36
- config-functional ootb
  rodvrees
  committed
  0de75d4
- Runnable with mzml flag
  rodvrees
  committed
  923a2cd
Commits on Aug 6, 2025
- Adapt fasta based on cmd line
  rodvrees
  committed
  0945c23
- gather correct pickles
  rodvrees
  committed
  2ee6561
Commits on Aug 7, 2025
- Further IO improvements
  rodvrees
  committed
  d368ace
Commits on Aug 8, 2025
- Merge pull request #2 from CompOmics/run-ootb
  RobbinBouwmeester
  authored
  02b2433
- change configuration
  RobbinBouwmeester
  committed
  6e06a1e
- Merge branch 'main' of github.com:compomics/MuMDIA
  RobbinBouwmeester
  committed
  f46968d
- New config
  RobbinBouwmeester
  committed
  406c7e4
- New config
  RobbinBouwmeester
  committed
  4b24e2a
- Change config
  RobbinBouwmeester
  committed
  2dafbca
- New config
  RobbinBouwmeester
  committed
  4ead005
Commits on Aug 11, 2025
- fix outfile.pin path
  rodvrees
  committed
  95b7b0b
- Merge branch 'main' into run-ootb
  rodvrees
  authored
  11c8937
- Merge pull request #3 from CompOmics/run-ootb
  rodvrees
  authored
  226b8d0
Commits on Aug 13, 2025
- Fix intensity correlation bug
  rodvrees
  committed
  2b0039f
- update .gitignore
  rodvrees
  committed
  b357eef
- update
  rodvrees
  committed
  d095838
- update pyproject.toml
  rodvrees
  committed
  c63cada
- Fix running with new config
  rodvrees
  committed
  d9bdfcc
- Prevent df_psms explosion because of merging on peptide
  rodvrees
  committed
  99083d9
Commits on Aug 18, 2025
- Fix peptide_max bug, potentially messing up other stuff
  rodvrees
  committed
  78e5187
Commits on Aug 19, 2025
- Plotting utils
  rodvrees
  committed
  ae1af0b
Commits on Aug 20, 2025
- Merge pull request #4 from CompOmics/run-ootb
  RobbinBouwmeester
  authored
  e68c2b6
- add coefficient_bounds
  rodvrees
  committed
  330065a
- Add coefficient_bounds param
  rodvrees
  committed
  e9ccb41
Commits on Aug 25, 2025
- updates
  rodvrees
  committed
  274816a
Commits on Sep 2, 2025
- Rewrite configuration system: unified, clean, type-safe approach
  RobbinBouwmeester
  committed
  95d590f
- Remove lazy imports and add conda environment check
  RobbinBouwmeester
  committed
  daeb9ac
- Remove llm blabber
  RobbinBouwmeester
  committed
  28248b7
- Fix configuration field name inconsistency
  RobbinBouwmeester
  committed
  d0f2098
- Refactor initial search into separate function
  RobbinBouwmeester
  committed
  9de3e17
- Refactor targeted search (Stage 2) into separate function
  RobbinBouwmeester
  committed
  65949c4
- Update configuration and plotting defaults
  RobbinBouwmeester
  committed
  8a0a595
Commits on Sep 3, 2025
- Remove all empty files from repository
  RobbinBouwmeester
  committed
  861ee5a
- Add DIA-NN features
  rodvrees
  committed
  3c1b12b
- feat: Implement simplified config system with backwards compatibility
  RobbinBouwmeester
  committed
  d45c0a1
- refactor: Replace old config system with new simplified system
  RobbinBouwmeester
  committed
  4a8fb70
Commits on Sep 5, 2025
- Add DIA-NN feature generator
  rodvrees
  committed
  0c0ab89
Commits on Sep 9, 2025
- add retention time margins to PSM df before calculating features
  Cajac102
  committed
  1757374
Commits on Sep 11, 2025
- add fragment name col earlier
  Cajac102
  committed
  c0d1725
- add fragment name col earlier
  Cajac102
  committed
  1c9b92f
- add rt margins, and plot histogram of top100 in debug folder
  Cajac102
  committed
  4681afc
- remove prints
  Cajac102
  committed
  5cffd75
- set default intensity cutoff to 5%
  Cajac102
  committed
  eb41c64
- also add rt margins to df_fragment
  Cajac102
  committed
  fbb2ec1
Commits on Sep 15, 2025
- add baseline lfq fragment, peptide, and protein quantification methods
  Cajac102
  committed
  f00d0bc
- remove TODO comment
  Cajac102
  committed
  b7afea3
Commits on Sep 17, 2025
- Merge pull request #8 from CompOmics/run-ootb
  RobbinBouwmeester
  authored
  85505c9
Commits on Sep 19, 2025
- add stripped peptide to fragment df
  Cajac102
  committed
  83989c2
Commits on Sep 22, 2025
- improve speed
  Cajac102
  committed
  86bdd5b
Commits on Sep 26, 2025
- only do fragment quantification in mumDIA, protein Quant with directLFQ
  Cajac102
  committed
  325df4b
- filter quant for peptides q-val < 0.01
  Cajac102
  committed
  3133bb3
- add mods to quant file, add test ipynb
  Cajac102
  committed
  6197ede
- Merge branch 'main' into add_retention_time_margins
  Cajac102
  committed
  6982bfa
- Update run.py
  
  Cajac102
  and
  Copilot
  authored
  3218013
- Update run.py
  
  Cajac102
  and
  Copilot
  authored
  e3edeb0
- Update mumdia.py
  
  Cajac102
  and
  Copilot
  authored
  08800a6
Commits on Sep 29, 2025
- remove old import
  Cajac102
  committed
  af27b44
Commits on Oct 1, 2025
Commits on Oct 2, 2025
- Fix test failures: uncomment CorrelationResults fields and remove interactive input from pickling
  RobbinBouwmeester
  committed
  7bd5332
Commits on Oct 9, 2025
- Update pyproject.toml
  RobbinBouwmeester
  authored
  fc6a10c
Commits on Oct 24, 2025
- remove hardcoded feature number
  Cajac102
  committed
  fbc902f

Commits

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